boxavg(1) General Commands Manual boxavg(1)
NAME
boxavg - averages images from specified locations in an image file
SYNOPSIS
boxavg [options] image_input_file model_input_file average_out-
put_file
DESCRIPTION
Boxavg will average images at points specified in an IMOD model file.
By default, it take all points from open contour and scattered point
objects, but specific objects can be selected instead. After computing
an average, it can then align each extracted image with the average by
searching for the shift that minimizes the standard deviation of the
difference between the two.
OPTIONS
Boxavg uses the PIP package for input exclusively (see the manual page
for pip). The following options can be specified either as command
line arguments (with the -) or one per line in a command file or param-
eter file (without the -). Options can be abbreviated to unique let-
ters; the currently valid abbreviations for short names are shown in
parentheses.
-image (-i) OR -InputImageFile File name
Input file with images containing features to average. If this
option is not entered, the first non-option argument will be
used for this input file.
-points (-po) OR -PointModelFile File name
Name of model file with points to be averaged. If this option
is not entered, the second non-option argument will be used for
this input file.
-output (-ou) OR -OutputFile File name
Output file for average image. If this option is not entered,
the third non-option argument will be used for this output file.
-piece (-pi) OR -PieceListFile File name
Name of piece list file if image is montaged or out of sequence
-objects (-ob) OR -ObjectsToAverage List of integer ranges
List of objects with points to average (comma-separated ranges
allowed). The default is to take all points from all open con-
tour or scattered point objects. This option can be used to
select a subset of objects in the model or force the use of a
closed contour object.
-box (-b) OR -BoxSizeXandY Two integers
Size of box to average in X and Y
-mode (-m) OR -ModeOfOutput Integer
Mode for output: 0 for byte, 1 for integer, 2 for 32-bit float,
6 for unsigned integer, or 12 for 16-bit float. The default is
the same as that of the input, although the default mode of
floating point output for MRC files is governed by the value of
environment variable IMOD_WRITE_FLOATS_16BIT. Mode 12 is
allowed only if the output format is MRC.
-passes (-pas) OR -PassesThroughData Integer
Number of passes through the data, either 1 or 2. On the second
pass, the boxes will be aligned to the average from the first
pass. The default is 2; enter 1 to skip the alignment pass.
-linear (-l) OR -LinearInterpolation
Use linear instead of cubic interpolation when extracting box
OBSOLETE OPTIONS
These options are not needed when Xcorrstack is used to correlate
an average with images.
-size (-si) OR -SizeOfOutputXandY Two integers
Size of output file in X and Y (default is same size as box)
-fill (-f) OR -FillValue Floating point
Value to fill with when output array is bigger than box. The
default is the mean along the edge of the average image. This
entry is ignored if the output is the same size as the box.
-split (-sp) OR -SplitIntoCorners
Split average into the four corners of the output array
-zero (-z) OR -ZeroMean
Shift the output to have a zero mean value. This option is
ignored if the data mode of the output is bytes or unsigned
integers.
-param (-par) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde, 4/26/89
Converted to PIP, using a model file and non-integer coordinates,
10/21/07
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 boxavg(1)